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VPS35L VPS35 endosomal protein sorting factor like [ Homo sapiens (human) ]

Gene ID: 57020, updated on 5-Mar-2024

Summary

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Official Symbol
VPS35Lprovided by HGNC
Official Full Name
VPS35 endosomal protein sorting factor likeprovided by HGNC
Primary source
HGNC:HGNC:24641
See related
Ensembl:ENSG00000103544 MIM:618981; AllianceGenome:HGNC:24641
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EC97; RTSC3; C16orf62
Summary
Involved in Golgi to plasma membrane transport and endocytic recycling. Located in endosome. Implicated in Ritscher-Schinzel syndrome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 13.6), brain (RPKM 13.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16p12.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19555703..19701163)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19486575..19631965)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (19567025..19712485)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19532887-19533621 Neighboring gene glycerophosphodiester phosphodiesterase 1 Neighboring gene centriolar coiled-coil protein 110 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19566659-19567621 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:19620544-19621743 Neighboring gene NANOG hESC enhancer GRCh37_chr16:19673654-19674240 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19698132-19698632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710103-19710758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710759-19711413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721101-19721825 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19721826-19722552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:19723278-19724003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10534 Neighboring gene lysine rich nucleolar protein 1 Neighboring gene IQ motif containing K Neighboring gene uncharacterized LOC105371115

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome. Otsuji S, et al. J Med Genet, 2023 Apr. PMID 36113987, Free PMC Article
  2. Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex. Kato K, et al. J Med Genet, 2020 Apr. PMID 31712251
  3. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Phillips-Krawczak CA, et al. Mol Biol Cell, 2015 Jan 1. PMID 25355947, Free PMC Article
  4. Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. Naukkarinen J, et al. PLoS Genet, 2010 Jun 3. PMID 20532202, Free PMC Article
  5. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. McNally KE, et al. Nat Cell Biol, 2017 Oct. PMID 28892079, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome.
    Title: Clinical diversity and molecular mechanism of VPS35L-associated Ritscher-Schinzel syndrome.
  2. Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex.
    Title: Biallelic VPS35L pathogenic variants cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex.
  3. Heterotrimer composed of DSCR3, C16orf62 and VPS29 orchestrates endosomal cargo retrieval and recycling.
    Title: Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Ritscher-Schinzel syndrome 3
MedGen: C5436883 OMIM: 619135 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21040, MGC16824, DKFZp313M0539, DKFZp434B0212

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi to plasma membrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endocytic recycling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
VPS35 endosomal protein-sorting factor-like
Names
UPF0505 protein C16orf62
esophageal cancer associated protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001300743.3 → NP_001287672.2  VPS35 endosomal protein-sorting factor-like isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621, AK095078
    Consensus CDS
    CCDS73840.1
    UniProtKB/TrEMBL
    B3KT69, F5H7K1
    Related
    ENSP00000442468.2, ENST00000542263.5

  2. NM_001365293.2 → NP_001352222.1  VPS35 endosomal protein-sorting factor-like isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621
    UniProtKB/TrEMBL
    B3KT69

  3. NM_001365294.2 → NP_001352223.1  VPS35 endosomal protein-sorting factor-like isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621
    UniProtKB/TrEMBL
    B3KT69

  4. NM_001365295.2 → NP_001352224.1  VPS35 endosomal protein-sorting factor-like isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621
    UniProtKB/TrEMBL
    H3BV68
    Related
    ENSP00000457973.1, ENST00000543152.5

  5. NM_020314.7 → NP_064710.5  VPS35 endosomal protein-sorting factor-like isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC002550, AK290286, AL136744, BP219237, DA452318
    Consensus CDS
    CCDS32397.3
    UniProtKB/Swiss-Prot
    A8K2M1, O43329, Q69YI1, Q6PDA0, Q7L371, Q7Z3J2, Q86W66, Q8WXA5, Q9H0L7, Q9H7C8
    UniProtKB/TrEMBL
    E7EWW0
    Related
    ENSP00000395973.3, ENST00000417362.7

RNA

  1. NR_158160.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621

  2. NR_158161.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC002550, AC012621

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    19555703..19701163
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    19486575..19631965
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z3J2.2 GenPept UniProtKB/Swiss-Prot:Q7Z3J2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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